LONDON -- South African scientists identified a new version of the coronavirus this week that they say is behind a recent spike in Covid-19 infections in Gauteng, the country’s most populous province.
It's unclear where the new variant first emerged, but scientists in South Africa first alerted the World Health Organization and it has now been seen in travelers to Belgium, Botswana, Hong Kong and Israel.
South African Health Minister Joe Phaahla said the variant was linked to an “exponential rise” of cases in the last few days, although experts are still trying to determine if the new variant is actually responsible.
From just over 200 new confirmed cases per day in recent weeks, South Africa saw the number of new daily cases rocket to 2,465 on Thursday. Struggling to explain the sudden rise in cases, scientists studied virus samples from the outbreak and discovered the new variant.
In a statement on Friday, the WHO designated it as a “variant of concern,” naming it “omicron” after a letter in the Greek alphabet.
After convening a group of experts to assess the data, the U.N. health agency said that “preliminary evidence suggests an increased risk of reinfection with this variant,” as compared to other variants.
“The number of cases of this variant appears to be increasing in almost all provinces in South Africa,” the WHO said.
Why are scientists worried?
It appears to have a high number of mutations — about 30 — in the coronavirus’ spike protein, which could affect how easily it spreads to people.
Sharon Peacock, who has led genetic sequencing of Covid-19 in Britain at the University of Cambridge, said the data so far suggest the new variant has mutations “consistent with enhanced transmissibility,” but said that “the significance of many of the mutations is still not known.”
Lawrence Young, a virologist at the University of Warwick, described omicron as “the most heavily mutated version of the virus we have seen," including potentially worrying changes never before seen all in the same virus.
Dr. Anthony Fauci, the U.S.' top infectious diseases doctor, said American officials had arranged a call with their South African counterparts later on Friday to find out more details and said there was no indication the variant had yet arrived in the U.S.
What's known and not known
Scientists know that omicron is genetically distinct from previous variants including the beta and delta variants, but do not know if these genetic changes make it any more transmissible or dangerous. So far, there is no indication the variant causes more severe disease.
It will likely take weeks to sort out if omicron is more infectious and if vaccines are still effective against it.
Peter Openshaw, a professor of experimental medicine at Imperial College London said it was “extremely unlikely” that current vaccines wouldn’t work, noting they are effective against numerous other variants.
Even though some of the genetic changes in omicron appear worrying, it's still unclear if they will pose a public health threat. Some previous variants, like the beta variant, initially alarmed scientists but didn't end up spreading very far.
“We don’t know if this new variant could get a toehold in regions where delta is,” said Peacock of the University of Cambridge. “The jury is out on how well this variant will do where there are other variants circulating.” To date, delta is by far the most predominant form of Covid-19, accounting for more than 99% of sequences submitted to the world’s biggest public database.
How did 'omicron' arise?
The coronavirus mutates as it spreads and many new variants, including those with worrying genetic changes, often just die out.
Scientists monitor Covid-19 sequences for mutations that could make the disease more transmissible or deadly, but they cannot determine that simply by looking at the virus.
Peacock said the variant “may have evolved in someone who was infected but could then not clear the virus, giving the virus the chance to genetically evolve," in a scenario similar to how experts think the alpha variant — which was first identified in England — also emerged, by mutating in an immune-compromised person.
Are the travel restrictions justified?
Maybe. As of noon Friday, travelers arriving in the U.K. from South Africa, Namibia, Botswana, Lesotho, Eswatini and Zimbabwe will have to self-isolate for 10 days. European Union nations also moved quickly on Friday to ban air travel from southern Africa, and the U.S. also said it would ban travel from South Africa and seven other African nations by non-US citizens beginning Monday, November 29.
Australian officials were racing Sunday, November 28, to conduct further tests on passengers arriving from southern Africa who tested positive for Covid-19 to determine if they were carrying the omicron variant as nations around the world tightened controls against the worrying new strain.
New Zealand announced it was restricting travel from nine southern African countries because of the threat posed by the variant, and Japan widened its border controls to include more countries from the region. Tourist-dependent Thailand, which only recently began loosening its tight border restrictions to leisure travelers from certain countries, announced a ban of its own on visitors from eight African counties. Similar restrictions took effect in the business hub of Singapore, which is barring entry and transit to anyone with a recent history of travel to seven southern African nations.
The tighter restrictions in the Asia-Pacific region echoed steps rapidly taken by countries around the world to limit the spread of the omicron variant just days after it was identified by researchers in South Africa.
Other countries that have slapped restrictions on various southern African countries over the past couple of days, including Australia, Brazil, Canada, the European Union, Iran, Japan, New Zealand, Thailand and the United States, in response to warnings over the transmissibility of the new variant.
Given the recent rapid rise in Covid-19 in South Africa, restricting travel from the region is “prudent” and would buy authorities more time, said Neil Ferguson, an infectious diseases expert at Imperial College London.
Jeffrey Barrett, director of Covid-19 Genetics at the Wellcome Sanger Institute, thought that the early detection of the new variant could mean restrictions taken now would have a bigger impact than when the delta variant first emerged
“With delta, it took many, many weeks into India’s terrible wave before it became clear what was going on and delta had already seeded itself in many places in the world and it was too late to do anything about it,” he said. “We may be at an earlier point with this new variant so there may still be time to do something about it.”
PH response
In response to the detection of a new variant, the Philippine government ordered Friday, November 26, the temporary suspension of inbound flights from South Africa and six other countries to prevent the entry of B.1.1.529, a new variant of Sars-CoV-2, which causes the coronavirus disease (Covid-19).
In its Resolution 150-D, the Inter-Agency Task Force (IATF) for the Management of Emerging Infectious Diseases said the B.1.1.529 variant, also known as omicron, has now been classified as a variant under monitoring.
"Upon the recommendations of its Technical Working Group on Covid-19 Variants, and favorable recommendation of the Department of Health and Department of Foreign Affairs, the border control measures to prevent the entry of the B.1.1.529 variant, which have the potential for increased transmissibility and effect in vaccine efficacy, shall be implemented," said the IATF.
Inbound international flights from South Africa, Botswana, Namibia, Zimbabwe, Lesotho, Eswatini and Mozambique were temporarily suspended effective immediately and until December 15, 2021, it added.
The Bureau of Quarantine was tasked to closely coordinate with local government units (LGUs) and locate travelers from the above-mentioned countries who may have arrived in the recent seven days prior to the temporary suspension of inbound travel.
"These travelers shall be required to undergo full 14-day facility-based quarantine with RT-PCR test on the seventh day or upon location of the passenger, whichever is later, with date of arrival as Day 1," said the IATF.
Passengers coming from or having been to those countries within the last 14 days prior to arrival are also temporarily barred from entering the Philippines.
The IATF clarified, however, that those who are already in transit from those countries, and have been to those territories within the last 14 days immediately preceding arrival to the Philippines and who arrive before November 28 will not be subjected to the above restrictions.
They, however, will be required to undergo stricter quarantine and testing protocols, which include the observation of an "absolute facility-based 14-day quarantine period, notwithstanding a negative RT-PCR result."
All passengers, whether Filipinos or foreigners, who are merely transiting through the countries mentioned above wil be deemed as having come from or having been to those areas if they stayed in the airport the whole time and were not cleared for entry by the immigration authorities.
It added that passengers covered by the measure are required to comply with the existing testing and quarantine protocols.
Meanwhile, National Task Force (NTF) Against Covid-19 spokesperson Restituto Padilla said on Sunday, November 28, 2021 that the government has temporarily banned incoming flights from Hong Kong.
"Bi-nan po lahat ng country na may na-detect na variant. So Hong Kong, may na-detect po diyan, so kasama na rin po iyon (All countries where the Omicron variant was detected have been banned, including Hong Kong)," he said.
“Ang movement po ng Filipino ay hindi pinagbabawal. Pero 'yong flight na kanilang sasakyan na papunta dito, pinagbabawal. So kung wala silang masasakyan, wala rin silang means para makarating (The movement of Filipinos is allowed, but the flights going to the Philippines from those countries have been banned, so they also have no means of entering the country)," he added.
However, the NTF released a statement hours later that the statement made by Padilla on the ban on flights from Hong Kong was not yet final.
“We await the formal announcement from the IATF (Inter-Agency Task Force) following a final recommendation from the Technical Working Group on Covid-19 Variants and other agencies. The Government through favorable recommendations of the Department of Health (DOH) will work to ensure timely adoption of preemptive measures to prevent or delay the entry of new variants which have the potential for undermining public health,” the NTF said in a statement.
“Until a formal announcement from the IATF is made, HK (Hong Kong) flights will still be allowed. We apologize for any inconvenience an earlier pronouncement may have caused,” it added.
Spreading
The new potentially more contagious omicron variant of the coronavirus popped up in more European countries on Saturday, just days after being identified in South Africa, leaving governments around the world scrambling to stop the spread.
The U.K. on Saturday tightened its rules on mask-wearing and on testing of international arrivals after finding two cases. New cases were confirmed Saturday in Germany and Italy, with Belgium, Israel and Hong Kong also reporting that the variant has been found in travelers.
In the U.S., Fauci, the government’s top infectious diseases expert, said he would not be surprised if the omicron variant was already in the United States, too.
“We have not detected it yet, but when you have a virus that is showing this degree of transmissibility ... it almost invariably is ultimately going to go essentially all over,” Fauci said on NBC television.
In Britain, Prime Minister Boris Johnson said it was necessary to take “targeted and precautionary measures” after two people tested positive for the new variant in England.
“Right now this is the responsible course of action to slow down the seeding and the spread of this new variant and to maximize our defenses,” he told a news conference.
Britain's Department of Health said the two cases found in the U.K. were linked and involved travel from southern Africa.
Italy and Germany were the latest to report confirmed cases of the omicron variant.
An Italian who had traveled to Mozambique on business landed in Rome on Nov. 11 and returned to his home near Naples. He and five family members, including two school-age children, have since tested positive, the Italian news agency LaPresse said. All are isolating in the Naples suburb of Caserta in good condition with light symptoms.
The variant was confirmed by Sacco hospital in Milan, and Italy’s National Health Institute said the man had received two doses of the vaccine. Italy’s health ministry is urging all regions to increase its tracing of the virus and sequencing to detect cases of the new variant first identified in South Africa.
In Germany, the Max von Pettenkofer Institute, a Munich-based microbiology center, said the omicron variant was confirmed in two travelers who arrived on a flight from South Africa on Nov. 24. The head of the institute, Oliver Keppler, said that genome sequencing has yet to be completed, but it is “proven without doubt that it is this variant,” German news agency dpa reported.
The Dutch public health institute said the omicron variant was “probably found in a number of the tested persons” who were isolated after arriving Friday in Amsterdam on two flights from South Africa. The institute said in a statement that further sequencing analysis is underway to determine for sure that it is the new variant. The results were expected Sunday. A total of 61 people were tested.
Israel said it detected the new strain in a traveler who had returned from Malawi and was tracing 800 travelers who returned recently from southern African countries. And Australia said early Sunday its scientists were working to determine whether two people who tested positive for Covid after arriving from southern Africa are infected with the omicron variant.
Vaccines
A number of pharmaceutical firms, including AstraZeneca, Moderna, Novavax and Pfizer, said they have plans in place to adapt their vaccines in light of the emergence of omicron. Pfizer and its partner BioNTech said they expect to be able to tweak their vaccine in around 100 days.
Professor Andrew Pollard, the director of the Oxford Vaccine Group, which developed the AstraZeneca vaccine, expressed cautious optimism that existing vaccines could be effective at preventing serious disease from the omicron variant, noting that most of the mutations appear to be in similar regions as those in other variants.
“At least from a speculative point of view we have some optimism that the vaccine should still work against a new variant for serious disease, but really we need to wait several weeks to have that confirmed," he told BBC radio.
Some experts said the variant’s emergence illustrated how rich countries’ hoarding of vaccines threatens to prolong the pandemic.
Fewer than 6% of people in Africa have been fully immunized against Covid-19, and millions of health workers and vulnerable populations have yet to receive a single dose. Those conditions can speed up spread of the virus, offering more opportunities for it to evolve into a dangerous variant.
“One of the key factors to emergence of variants may well be low vaccination rates in parts of the world, and the WHO warning that none of us is safe until all of us are safe and should be heeded," said Peter Openshaw, a professor of experimental medicine at Imperial College London. (Pooled reports from AP and SunStar Philippines)